NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5343406 Query DataSets for GSM5343406
Status Public on May 24, 2024
Title Lane1_Sample_13
Sample type SRA
 
Source name Whole Blood
Organism Mus musculus
Characteristics tissue: Whole Blood
lane.ordinal: 13
mouse: 51
infection.time.point.days: 14
age.days: 92
cage: 20
tb.status: naive
aerosol.run: NA
strain: Balb/c
lung.cfus: NA
blood.source: Heart
sequencing.lane: 1
Extracted molecule genomic DNA
Extraction protocol Whole blood was collected, mixed with EDTA, and mixed with Zymo Research DNA/RNA Shield. DNA was isolated using the Zymo Research Quick-DNA kit and Genomic DNA Clean & Concentrator kit.
Libraries were prepared using Reduced Representation Bisulfite Sequencing. 52 samples were pooled together using custom synthesized methylated adapters with unique dual indexes (Integrated DNA Technologies).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina NovaSeq 6000
 
Data processing Basecalls performed using bcl2fastq2 v.2.19
Adapter removal and quality trimming were performed by using Trim Galore! v.0.6.4
Alignment performed by BitMapperBS v.1.0.2.3 with default options: bitmapperBS --search ${REFERENCE} --seq1 ${R1} --seq2 ${R2} --bam -o Sample_${n}.bam
Methylation levels were determined using MethylDackel v.0.4.0 with default options: MethylDackel extract $DACKELREFERENCE $bam_file
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Processed files are MethylDackel bedGraph output files with 1. Chromosome name 2. Start coordinate 3. End coordinate 4. Methylation percentage 5. Number of alignments reporting methylated bases 6. Number of alignments reporting unmethylated bases
 
Submission date May 27, 2021
Last update date May 24, 2024
Contact name Russell Ault
Organization name The Ohio State University College of Medicine
Street address 370 W 9th Ave
City Columbus
State/province OH
ZIP/Postal code 43210
Country USA
 
Platform ID GPL24247
Series (1)
GSE175661 Blood DNA methylation altered by Mycobacterium tuberculosis infection in mice
Relations
BioSample SAMN19369697
SRA SRX11006564

Supplementary file Size Download File type/resource
GSM5343406_Lane1_Sample_13.bam.sorted_CpG.bedGraph.gz 25.6 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap